PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Metabarcoding of the phytotelmata of Pseudalcantarea grandis (Bromeliaceae) from an arid zone
items: Beyond RuBisCO: convergent molecular evolution of multiple chloroplast genes in C4 plants
items: Soil health and nutrient density: preliminary comparison of regenerative and conventional farming
items: Effects of inorganic mercury exposure in the alveolar bone of rats: an approach of qualitative and morphological aspects
items: miR-148a-3p inhibits the proliferation and migration of bladder cancer via regulating the expression of ROCK-1
items: The performance of body mass component indices in detecting risk of musculoskeletal injuries in physically active young men and women
items: Comparison of the bleaching susceptibility of coral species by using minimal samples of live corals
items: Potential impacts from simulated vessel noise and sonar on commercially important invertebrates
items: Isolation, identification and characterization of nitrogen fixing endophytic bacteria and their effects on cassava production
items: Diversity and structure of the microbial community in rhizosphere soil of Fritillaria ussuriensis at different health levels

Metabarcoding of the phytotelmata of Pseudalcantarea grandis (Bromeliaceae) from an arid zone
type: item
type: AcademicArticle
description: Background Pseudalcantarea grandis (Schltdl.) Pinzón & Barfuss is a tank bromeliad that grows on cliffs in the southernmost portion of the Chihuahuan desert. Phytotelmata are water bodies formed by plants that function as micro-ecosystems where bacteria, algae, protists, insects, fungi, and some vertebrates can develop. We hypothesized that the bacterial diversity contained in the phytotelma formed in a bromeliad from an arid zone would differ in sites with and without surrounding vegetation. Our study aimed to characterize the bacterial composition and putative metabolic functions in P. grandis phytotelmata collected in vegetated and non-vegetated sites. Methods Water from 10 individuals was sampled. Five individuals had abundant surrounding vegetation, and five had little or no vegetation. We extracted DNA and amplified seven hypervariable regions of the 16S gene (V2, V4, V8, V3–6, 7–9). Metabarcoding sequencing was performed on the Ion Torrent PGM platform. Taxonomic identity was assigned by the binning reads and coverage between hit and query from the reference database of at least 90%. Putative metabolic functions of the bacterial families were assigned mainly using the FAPROTAX database. The dominance patterns in each site were visualized with rank/abundance curves using the number of Operational Taxonomic Units (OTUs) per family. A percentage similarity analysis (SIMPER) was used to estimate dissimilarity between the sites. Relationships among bacterial families (identified by the dominance analysis and SIMPER), sites, and their respective putative functions were analyzed with shade plots. Results A total of 1.5 million useful bacterial sequences were obtained. Sequences were clustered into OTUs, and taxonomic assignment was conducted using BLAST in the Greengenes databases. Bacterial diversity was 23 phyla, 52 classes, 98 orders, 218 families, and 297 genera. Proteobacteria (37%), Actinobacteria (19%), and Firmicutes (15%) comprised the highest percentage (7…
format: application/pdf
format: text/html
creator: José Alan Herrera-García
creator: Mahinda Martinez
creator: Pilar Zamora-Tavares
creator: Ofelia Vargas-Ponce
creator: Luis Hernández-Sandoval
creator: Fabián Alejandro Rodríguez-Zaragoza
subject: Biodiversity
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.12706
publisher: PeerJ Inc.
rights: © 2022 Herrera-García et al.
abstract: Background Pseudalcantarea grandis (Schltdl.) Pinzón & Barfuss is a tank bromeliad that grows on cliffs in the southernmost portion of the Chihuahuan desert. Phytotelmata are water bodies formed by plants that function as micro-ecosystems where bacteria, algae, protists, insects, fungi, and some vertebrates can develop. We hypothesized that the bacterial diversity contained in the phytotelma formed in a bromeliad from an arid zone would differ in sites with and without surrounding vegetation. Our study aimed to characterize the bacterial composition and putative metabolic functions in P. grandis phytotelmata collected in vegetated and non-vegetated sites. Methods Water from 10 individuals was sampled. Five individuals had abundant surrounding vegetation, and five had little or no vegetation. We extracted DNA and amplified seven hypervariable regions of the 16S gene (V2, V4, V8, V3–6, 7–9). Metabarcoding sequencing was performed on the Ion Torrent PGM platform. Taxonomic identity was assigned by the binning reads and coverage between hit and query from the reference database of at least 90%. Putative metabolic functions of the bacterial families were assigned mainly using the FAPROTAX database. The dominance patterns in each site were visualized with rank/abundance curves using the number of Operational Taxonomic Units (OTUs) per family. A percentage similarity analysis (SIMPER) was used to estimate dissimilarity between the sites. Relationships among bacterial families (identified by the dominance analysis and SIMPER), sites, and their respective putative functions were analyzed with shade plots. Results A total of 1.5 million useful bacterial sequences were obtained. Sequences were clustered into OTUs, and taxonomic assignment was conducted using BLAST in the Greengenes databases. Bacterial diversity was 23 phyla, 52 classes, 98 orders, 218 families, and 297 genera. Proteobacteria (37%), Actinobacteria (19%), and Firmicutes (15%) comprised the highest percentage (7…
bibliographic citation: Herrera-García et al. (2022) Metabarcoding of the phytotelmata of Pseudalcantarea grandis (Bromeliaceae) from an arid zone. PeerJ 10:e12706 https://doi.org/10.7717/peerj.12706
date submitted: 2021-02-17
date accepted: 2021-12-07
issued: 2022-01-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Herrera-García
  given name: José Alan
author list: Agent
  family name: Martinez
  given name: Mahinda
author list: Agent
  family name: Zamora-Tavares
  given name: Pilar
author list: Agent
  family name: Vargas-Ponce
  given name: Ofelia
author list: Agent
  family name: Hernández-Sandoval
  given name: Luis
author list: Agent
  family name: Rodríguez-Zaragoza
  given name: Fabián Alejandro
doi: 10.7717/peerj.12706
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-27
copyright: © 2022 Herrera-García et al.
attribution name: Herrera-García et al.

Beyond RuBisCO: convergent molecular evolution of multiple chloroplast genes in C4 plants
type: item
type: AcademicArticle
description: Background The recurrent evolution of the C4 photosynthetic pathway in angiosperms represents one of the most extraordinary examples of convergent evolution of a complex trait. Comparative genomic analyses have unveiled some of the molecular changes associated with the C4 pathway. For instance, several key enzymes involved in the transition from C3 to C4 photosynthesis have been found to share convergent amino acid replacements along C4 lineages. However, the extent of convergent replacements potentially associated with the emergence of C4 plants remains to be fully assessed. Here, we conducted an organelle-wide analysis to determine if convergent evolution occurred in multiple chloroplast proteins beside the well-known case of the large RuBisCO subunit encoded by the chloroplast gene rbcL. Methods Our study was based on the comparative analysis of 43 C4 and 21 C3 grass species belonging to the PACMAD clade, a focal taxonomic group in many investigations of C4 evolution. We first used protein sequences of 67 orthologous chloroplast genes to build an accurate phylogeny of these species. Then, we inferred amino acid replacements along 13 C4 lineages and 9 C3 lineages using reconstructed protein sequences of their reference branches, corresponding to the branches containing the most recent common ancestors of C4-only clades and C3-only clades. Pairwise comparisons between reference branches allowed us to identify both convergent and non-convergent amino acid replacements between C4:C4, C3:C3 and C3:C4 lineages. Results The reconstructed phylogenetic tree of 64 PACMAD grasses was characterized by strong supports in all nodes used for analyses of convergence. We identified 217 convergent replacements and 201 non-convergent replacements in 45/67 chloroplast proteins in both C4 and C3 reference branches. C4:C4 branches showed higher levels of convergent replacements than C3:C3 and C3:C4 branches. Furthermore, we found that more proteins shared unique convergent replacement…
format: application/pdf
format: text/html
creator: Claudio Casola
creator: Jingjia Li
subject: Agricultural Science
subject: Evolutionary Studies
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.12791
publisher: PeerJ Inc.
rights: © 2022 Casola and Li
abstract: Background The recurrent evolution of the C4 photosynthetic pathway in angiosperms represents one of the most extraordinary examples of convergent evolution of a complex trait. Comparative genomic analyses have unveiled some of the molecular changes associated with the C4 pathway. For instance, several key enzymes involved in the transition from C3 to C4 photosynthesis have been found to share convergent amino acid replacements along C4 lineages. However, the extent of convergent replacements potentially associated with the emergence of C4 plants remains to be fully assessed. Here, we conducted an organelle-wide analysis to determine if convergent evolution occurred in multiple chloroplast proteins beside the well-known case of the large RuBisCO subunit encoded by the chloroplast gene rbcL. Methods Our study was based on the comparative analysis of 43 C4 and 21 C3 grass species belonging to the PACMAD clade, a focal taxonomic group in many investigations of C4 evolution. We first used protein sequences of 67 orthologous chloroplast genes to build an accurate phylogeny of these species. Then, we inferred amino acid replacements along 13 C4 lineages and 9 C3 lineages using reconstructed protein sequences of their reference branches, corresponding to the branches containing the most recent common ancestors of C4-only clades and C3-only clades. Pairwise comparisons between reference branches allowed us to identify both convergent and non-convergent amino acid replacements between C4:C4, C3:C3 and C3:C4 lineages. Results The reconstructed phylogenetic tree of 64 PACMAD grasses was characterized by strong supports in all nodes used for analyses of convergence. We identified 217 convergent replacements and 201 non-convergent replacements in 45/67 chloroplast proteins in both C4 and C3 reference branches. C4:C4 branches showed higher levels of convergent replacements than C3:C3 and C3:C4 branches. Furthermore, we found that more proteins shared unique convergent replacement…
bibliographic citation: Casola et al. (2022) Beyond RuBisCO: convergent molecular evolution of multiple chloroplast genes in C4 plants. PeerJ 10:e12791 https://doi.org/10.7717/peerj.12791
date submitted: 2021-08-19
date accepted: 2021-12-22
issued: 2022-01-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Casola
  given name: Claudio
author list: Agent
  family name: Li
  given name: Jingjia
doi: 10.7717/peerj.12791
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-27
copyright: ©2022 Casola and Li
attribution name: Casola and Li

Soil health and nutrient density: preliminary comparison of regenerative and conventional farming
type: item
type: AcademicArticle
description: Several independent comparisons indicate regenerative farming practices enhance the nutritional profiles of crops and livestock. Measurements from paired farms across the United States indicate differences in soil health and crop nutrient density between fields worked with conventional (synthetically-fertilized and herbicide-treated) or regenerative practices for 5 to 10 years. Specifically, regenerative farms that combined no-till, cover crops, and diverse rotations—a system known as Conservation Agriculture—produced crops with higher soil organic matter levels, soil health scores, and levels of certain vitamins, minerals, and phytochemicals. In addition, crops from two regenerative no-till vegetable farms, one in California and the other in Connecticut, had higher levels of phytochemicals than values reported previously from New York supermarkets. Moreover, a comparison of wheat from adjacent regenerative and conventional no-till fields in northern Oregon found a higher density of mineral micronutrients in the regenerative crop. Finally, a comparison of the unsaturated fatty acid profile of beef and pork raised on one of the regenerative farms to a regional health-promoting brand and conventional meat from local supermarkets, found higher levels of omega-3 fats and a more health-beneficial ratio of omega-6 to omega-3 fats. Despite small sample sizes, all three crop comparisons show differences in micronutrient and phytochemical concentrations that suggest soil health is an under appreciated influence on nutrient density, particularly for phytochemicals not conventionally considered nutrients but nonetheless relevant to chronic disease prevention. Likewise, regenerative grazing practices produced meat with a better fatty acid profile than conventional and regional health-promoting brands. Together these comparisons offer preliminary support for the conclusion that regenerative soil-building farming practices can enhance the nutritional profile of conventionally gro…
format: application/pdf
format: text/html
creator: David R. Montgomery
creator: Anne Biklé
creator: Ray Archuleta
creator: Paul Brown
creator: Jazmin Jordan
subject: Agricultural Science
subject: Food Science and Technology
subject: Soil Science
description: doi:10.7717/peerj.12848
publisher: PeerJ Inc.
rights: © 2022 Montgomery et al.
abstract: Several independent comparisons indicate regenerative farming practices enhance the nutritional profiles of crops and livestock. Measurements from paired farms across the United States indicate differences in soil health and crop nutrient density between fields worked with conventional (synthetically-fertilized and herbicide-treated) or regenerative practices for 5 to 10 years. Specifically, regenerative farms that combined no-till, cover crops, and diverse rotations—a system known as Conservation Agriculture—produced crops with higher soil organic matter levels, soil health scores, and levels of certain vitamins, minerals, and phytochemicals. In addition, crops from two regenerative no-till vegetable farms, one in California and the other in Connecticut, had higher levels of phytochemicals than values reported previously from New York supermarkets. Moreover, a comparison of wheat from adjacent regenerative and conventional no-till fields in northern Oregon found a higher density of mineral micronutrients in the regenerative crop. Finally, a comparison of the unsaturated fatty acid profile of beef and pork raised on one of the regenerative farms to a regional health-promoting brand and conventional meat from local supermarkets, found higher levels of omega-3 fats and a more health-beneficial ratio of omega-6 to omega-3 fats. Despite small sample sizes, all three crop comparisons show differences in micronutrient and phytochemical concentrations that suggest soil health is an under appreciated influence on nutrient density, particularly for phytochemicals not conventionally considered nutrients but nonetheless relevant to chronic disease prevention. Likewise, regenerative grazing practices produced meat with a better fatty acid profile than conventional and regional health-promoting brands. Together these comparisons offer preliminary support for the conclusion that regenerative soil-building farming practices can enhance the nutritional profile of conventionally gro…
bibliographic citation: Montgomery et al. (2022) Soil health and nutrient density: preliminary comparison of regenerative and conventional farming. PeerJ 10:e12848 https://doi.org/10.7717/peerj.12848
date submitted: 2021-10-27
date accepted: 2022-01-07
issued: 2022-01-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Montgomery
  given name: David R.
author list: Agent
  family name: Biklé
  given name: Anne
author list: Agent
  family name: Archuleta
  given name: Ray
author list: Agent
  family name: Brown
  given name: Paul
author list: Agent
  family name: Jordan
  given name: Jazmin
doi: 10.7717/peerj.12848
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-27
copyright: © 2022 Montgomery et al.
attribution name: Montgomery et al.

Effects of inorganic mercury exposure in the alveolar bone of rats: an approach of qualitative and morphological aspects
type: item
type: AcademicArticle
description: Background In comparison to organic mercury (MeHg), the environmental inorganic mercury (IHg) can be found in some skin-lightening cosmestics were considered “harmless” for a long time. However, recent studies have shown that long-term exposure to low doses of IHg may affect biological systems. Therefore, this study investigated the effects of IHg long-term exposure to the alveolar bone of adult rats. Methods Adult Wistar rats were distributed in control and HgCl2 exposed (0.375 mg/kg/day). After 45 days, the rats were euthanized and both blood and hemimandibles were collected. Total blood Hg levels were measured and both inorganic and organic components of the alveolar bone were determined through XRD and ATR-FTIR. The microstructure of the alveolar bone was assessed by using micro-CT and the morphometric analysis was performed by using stereomicroscopy. Results Alterations in the physicochemical components of the alveolar bone of exposed animals were observed. The bone changes represented a tissue reaction at the microstructural level, such as bone volume increase. However, no significant dimensional changes (bone height) were observed. Conclusion Exposure to IHg at this dose can promote microstructural changes and alteration in the organic and inorganic components in the alveolar bone.
format: application/pdf
format: text/html
creator: Paula Beatriz de Oliveira Nunes
creator: Maria Karolina Martins Ferreira
creator: Deborah Ribeiro Frazão
creator: Leonardo Oliveira Bittencourt
creator: Victória dos Santos Chemelo
creator: Márcia Cristina Freitas Silva
creator: Armando Lopes Pereira-Neto
creator: Alan Rodrigo Leal Albuquerque
creator: Simone Patricia Aranha Paz
creator: Rômulo Simões Angélica
creator: Sofia Pessanha
creator: Rafael Rodrigues Lima
subject: Biochemistry
subject: Toxicology
description: doi:10.7717/peerj.12573
publisher: PeerJ Inc.
rights: © 2022 Nunes et al.
abstract: Background In comparison to organic mercury (MeHg), the environmental inorganic mercury (IHg) can be found in some skin-lightening cosmestics were considered “harmless” for a long time. However, recent studies have shown that long-term exposure to low doses of IHg may affect biological systems. Therefore, this study investigated the effects of IHg long-term exposure to the alveolar bone of adult rats. Methods Adult Wistar rats were distributed in control and HgCl2 exposed (0.375 mg/kg/day). After 45 days, the rats were euthanized and both blood and hemimandibles were collected. Total blood Hg levels were measured and both inorganic and organic components of the alveolar bone were determined through XRD and ATR-FTIR. The microstructure of the alveolar bone was assessed by using micro-CT and the morphometric analysis was performed by using stereomicroscopy. Results Alterations in the physicochemical components of the alveolar bone of exposed animals were observed. The bone changes represented a tissue reaction at the microstructural level, such as bone volume increase. However, no significant dimensional changes (bone height) were observed. Conclusion Exposure to IHg at this dose can promote microstructural changes and alteration in the organic and inorganic components in the alveolar bone.
bibliographic citation: Nunes et al. (2022) Effects of inorganic mercury exposure in the alveolar bone of rats: an approach of qualitative and morphological aspects. PeerJ 10:e12573 https://doi.org/10.7717/peerj.12573
date submitted: 2021-08-04
date accepted: 2021-11-09
issued: 2022-01-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nunes
  given name: Paula Beatriz de Oliveira
author list: Agent
  family name: Ferreira
  given name: Maria Karolina Martins
author list: Agent
  family name: Ribeiro Frazão
  given name: Deborah
author list: Agent
  family name: Bittencourt
  given name: Leonardo Oliveira
author list: Agent
  family name: Chemelo
  given name: Victória dos Santos
author list: Agent
  family name: Silva
  given name: Márcia Cristina Freitas
author list: Agent
  family name: Pereira-Neto
  given name: Armando Lopes
author list: Agent
  family name: Albuquerque
  given name: Alan Rodrigo Leal
author list: Agent
  family name: Paz
  given name: Simone Patricia Aranha
author list: Agent
  family name: Angélica
  given name: Rômulo Simões
author list: Agent
  family name: Pessanha
  given name: Sofia
author list: Agent
  family name: Lima
  given name: Rafael Rodrigues
doi: 10.7717/peerj.12573
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-26
copyright: © 2022 Nunes et al.
attribution name: Nunes et al.

miR-148a-3p inhibits the proliferation and migration of bladder cancer via regulating the expression of ROCK-1
type: item
type: AcademicArticle
description: Purpose To investigate the mechanism of miR-148a-3p regulating the proliferation and migration of bladder tumor cells. Materials and Methods We conducted a preliminary study to detect the relative expression of miR-148a-3p in bladder cancer and para-cancerous tissue samples. Three bladder tumor cell lines, T24, 5,637 and UM-UC-3, were selected. The expression levels of miR-148a-3p were artificially regulated with miR-148a-3p mimics and the miR-148a-3p inhibitor. The relative expression levels of miR-148a-3p in the samples of each cell line were determined. Cell Counting Kit-8 (CCK-8) was used to detect cell proliferation, while the effect of the miR-148a-3p mimics and inhibitor on tumor cell migration was detected by wound healing assay. Flow cytometry assay was carried out to explore the effect of miR-148a-3p on cell apoptosis. Dual-luciferase reporter assay was performed in order to verify miR-148a-3p’s target gene. The expressions of ROCK-1 and Bcl-2 were analyzed by western blot. Results The relative expression of miR-148a-3p in tumor and adjacent tissues was assessed with qRT-PCR (P < 0.05) and found to be significantly lower in the tumor tissues than the adjacent tissues. The data obtained from the CCK-8 and wound healing assay showed that intracellular transfection of miR-148a-3p mimics could inhibit cell proliferation and migration, while the miR-148a-3p inhibitor promoted them. Overexpression of miR-148a-3p promoted cell apoptosis in the T24 and 5,637 cell lines. The dual-luciferase reporter assay verified that ROCK-1 is a direct target of miR-148a-3p. Western blot showed that miR-148a-3p overexpression downregulated the expression of ROCK-1 and Bcl-2, while miR-148a-3p knockdown upregulated the expression of ROCK-1 and Bcl-2. Conclusions We confirmed that miR-148a-3p was significantly decreased in bladder cancer cells. miR-148a-3p overexpression inhibited bladder cancer cell proliferation and migration, whereas miR-148a-3p knockdown promoted bladder cancer…
format: application/pdf
format: text/html
creator: Chao Xu
creator: Guanwen Zhou
creator: Zhuang Sun
creator: Zhaocun Zhang
creator: Haifeng Zhao
creator: Xianzhou Jiang
subject: Cell Biology
subject: Molecular Biology
subject: Oncology
subject: Urology
description: doi:10.7717/peerj.12724
publisher: PeerJ Inc.
rights: © 2022 Xu et al.
abstract: Purpose To investigate the mechanism of miR-148a-3p regulating the proliferation and migration of bladder tumor cells. Materials and Methods We conducted a preliminary study to detect the relative expression of miR-148a-3p in bladder cancer and para-cancerous tissue samples. Three bladder tumor cell lines, T24, 5,637 and UM-UC-3, were selected. The expression levels of miR-148a-3p were artificially regulated with miR-148a-3p mimics and the miR-148a-3p inhibitor. The relative expression levels of miR-148a-3p in the samples of each cell line were determined. Cell Counting Kit-8 (CCK-8) was used to detect cell proliferation, while the effect of the miR-148a-3p mimics and inhibitor on tumor cell migration was detected by wound healing assay. Flow cytometry assay was carried out to explore the effect of miR-148a-3p on cell apoptosis. Dual-luciferase reporter assay was performed in order to verify miR-148a-3p’s target gene. The expressions of ROCK-1 and Bcl-2 were analyzed by western blot. Results The relative expression of miR-148a-3p in tumor and adjacent tissues was assessed with qRT-PCR (P < 0.05) and found to be significantly lower in the tumor tissues than the adjacent tissues. The data obtained from the CCK-8 and wound healing assay showed that intracellular transfection of miR-148a-3p mimics could inhibit cell proliferation and migration, while the miR-148a-3p inhibitor promoted them. Overexpression of miR-148a-3p promoted cell apoptosis in the T24 and 5,637 cell lines. The dual-luciferase reporter assay verified that ROCK-1 is a direct target of miR-148a-3p. Western blot showed that miR-148a-3p overexpression downregulated the expression of ROCK-1 and Bcl-2, while miR-148a-3p knockdown upregulated the expression of ROCK-1 and Bcl-2. Conclusions We confirmed that miR-148a-3p was significantly decreased in bladder cancer cells. miR-148a-3p overexpression inhibited bladder cancer cell proliferation and migration, whereas miR-148a-3p knockdown promoted bladder cancer…
bibliographic citation: Xu et al. (2022) miR-148a-3p inhibits the proliferation and migration of bladder cancer via regulating the expression of ROCK-1. PeerJ 10:e12724 https://doi.org/10.7717/peerj.12724
date submitted: 2021-03-02
date accepted: 2021-12-10
issued: 2022-01-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Xu
  given name: Chao
author list: Agent
  family name: Zhou
  given name: Guanwen
author list: Agent
  family name: Sun
  given name: Zhuang
author list: Agent
  family name: Zhang
  given name: Zhaocun
author list: Agent
  family name: Zhao
  given name: Haifeng
author list: Agent
  family name: Jiang
  given name: Xianzhou
doi: 10.7717/peerj.12724
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-26
copyright: © 2022 Xu et al.
attribution name: Xu et al.

The performance of body mass component indices in detecting risk of musculoskeletal injuries in physically active young men and women
type: item
type: AcademicArticle
description: Background Body composition indices can be related to musculoskeletal injuries (MI), particularly in physically active groups. However, little is known about the accuracy of these diagnoses as potential predictors of musculoskeletal injuries. Therefore, this study aims to indicate the cut-off points of relative body mass (BMI), fat mass index (FMI), skeletal muscle mass (SMI), and muscle to fat ratio (MFR) and establish its reliability in injury prediction for physically active men and women. Methods The sample included 119 physically active individuals aged 23.72 ± 1.12 (66 men body height 1.79 ± 0.07 (m); body weight 80.51 ± 9.85 (kg) and 53 women body height 1.67 ± 0.08 (m); body weight 62 ± 10.72 (kg)), students at university of physical education in Poland. The participants’ physical activity was measured with the International Physical Activity Questionnaire (IPAQ). The relevance of body mass index (BMI), fat mass index (FMI), skeletal muscle mass index (SMI), and muscle to fat ratio (MFR) in detecting injury risk was examined. Musculoskeletal injuries during 1 year before examination were registered using a self-reporting questionnaire. The areas under the curve (AUC) and Youden Index in the receiver operating characteristic curve (ROC) were calculated. Results The cut-off points used to classify the indices among men were BMI = 24.38; FMI = 3.74; SMI = 16.40; MFR = 3.70; and for women BMI = 20.90; FMI = 4.17; SMI = 8.96; MFR = 1.67. Results suggested the greatest reliability in the prediction of musculoskeletal injuries among men had BMI (AUC = 0.623; Youden = 0.30) and SMI (AUC = 0.608; Youden = 0.23) whereas among women, MFR (AUC = 0.628; Youden = 0.29) and FMI (AUC = 0.614; Youden = 0.32). Conclusion BMI and SMI are the most appropriate indices to predict the risk of musculoskeletal injury in physically active men, whereas in women, MFR and FMI are more reliable. These results indicate that the indices with more muscle mass meaning are better in predictin…
format: application/pdf
format: text/html
creator: Jarosław Domaradzki
creator: Dawid Koźlenia
subject: Kinesiology
subject: Environmental Health
subject: Sports Injury
subject: Sports Medicine
description: doi:10.7717/peerj.12745
publisher: PeerJ Inc.
rights: © 2022 Domaradzki and Koźlenia
abstract: Background Body composition indices can be related to musculoskeletal injuries (MI), particularly in physically active groups. However, little is known about the accuracy of these diagnoses as potential predictors of musculoskeletal injuries. Therefore, this study aims to indicate the cut-off points of relative body mass (BMI), fat mass index (FMI), skeletal muscle mass (SMI), and muscle to fat ratio (MFR) and establish its reliability in injury prediction for physically active men and women. Methods The sample included 119 physically active individuals aged 23.72 ± 1.12 (66 men body height 1.79 ± 0.07 (m); body weight 80.51 ± 9.85 (kg) and 53 women body height 1.67 ± 0.08 (m); body weight 62 ± 10.72 (kg)), students at university of physical education in Poland. The participants’ physical activity was measured with the International Physical Activity Questionnaire (IPAQ). The relevance of body mass index (BMI), fat mass index (FMI), skeletal muscle mass index (SMI), and muscle to fat ratio (MFR) in detecting injury risk was examined. Musculoskeletal injuries during 1 year before examination were registered using a self-reporting questionnaire. The areas under the curve (AUC) and Youden Index in the receiver operating characteristic curve (ROC) were calculated. Results The cut-off points used to classify the indices among men were BMI = 24.38; FMI = 3.74; SMI = 16.40; MFR = 3.70; and for women BMI = 20.90; FMI = 4.17; SMI = 8.96; MFR = 1.67. Results suggested the greatest reliability in the prediction of musculoskeletal injuries among men had BMI (AUC = 0.623; Youden = 0.30) and SMI (AUC = 0.608; Youden = 0.23) whereas among women, MFR (AUC = 0.628; Youden = 0.29) and FMI (AUC = 0.614; Youden = 0.32). Conclusion BMI and SMI are the most appropriate indices to predict the risk of musculoskeletal injury in physically active men, whereas in women, MFR and FMI are more reliable. These results indicate that the indices with more muscle mass meaning are better in predictin…
bibliographic citation: Domaradzki et al. (2022) The performance of body mass component indices in detecting risk of musculoskeletal injuries in physically active young men and women. PeerJ 10:e12745 https://doi.org/10.7717/peerj.12745
date submitted: 2021-10-04
date accepted: 2021-12-14
issued: 2022-01-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Domaradzki
  given name: Jarosław
author list: Agent
  family name: Koźlenia
  given name: Dawid
doi: 10.7717/peerj.12745
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-26
copyright: © 2022 Domaradzki and Koźlenia
attribution name: Domaradzki and Koźlenia

Comparison of the bleaching susceptibility of coral species by using minimal samples of live corals
type: item
type: AcademicArticle
description: In massive bleaching events (losing symbiotic algae from corals), more sensitive corals are bleached earlier than other corals. To perform a comparison of bleaching susceptibility within and across coral species, a simple quantitative method is required. Accordingly, we present a laboratory-based method for comparing the bleaching susceptibility of various coral species by using a standardized image analysis protocol. Coral fragments were sampled from the colonies of five species selected from Kenting, southern Taiwan, and maintained in the same aquarium tank with circulating seawater; 2 seawater temperature regimes were used (i.e., fast-heating program (FHP), with a heating rate of 1 °C per day; and slow-heating program (SHP), with a heating rate of 1 °C per 3 days). Each coral fragment was photographed periodically, and the colored images were subsequently converted to grayscale images and then digitally analyzed to determine the standardized grayscale values (G0) by comparing with that of standard color strip. The G0 of a sample at each time of photographing during bleaching was divided by the difference of G0 between the acclimating and the same but completely bleached fragment to derive the relative grayscale (RG%) at a particular stage of bleaching; this is done for each coral fragment of a colony. The smaller the RG% of a coral fragment the closer it is approaching completely bleached condition. The level of decrease in RG% within a time series of images in each heating regime was used to establish a bleaching time index (BTI). The lower the BTI, the sooner to reach a defined bleaching level (e.g., 30%), this indicates the coral is more sensitive to thermal bleaching. In the experiment, we compared the bleaching susceptibility of the five species. Based on the proposed BTI, the five species were ranked in terms of bleaching susceptibility, and the rankings were identical between the two temperature regimes; three species in Pocilloporidae had lower BTI, where…
format: application/pdf
format: text/html
creator: Jih-Terng Wang
creator: Chi-Wei Chu
creator: Keryea Soong
subject: Conservation Biology
subject: Marine Biology
description: doi:10.7717/peerj.12840
publisher: PeerJ Inc.
rights: © 2022 Wang et al.
abstract: In massive bleaching events (losing symbiotic algae from corals), more sensitive corals are bleached earlier than other corals. To perform a comparison of bleaching susceptibility within and across coral species, a simple quantitative method is required. Accordingly, we present a laboratory-based method for comparing the bleaching susceptibility of various coral species by using a standardized image analysis protocol. Coral fragments were sampled from the colonies of five species selected from Kenting, southern Taiwan, and maintained in the same aquarium tank with circulating seawater; 2 seawater temperature regimes were used (i.e., fast-heating program (FHP), with a heating rate of 1 °C per day; and slow-heating program (SHP), with a heating rate of 1 °C per 3 days). Each coral fragment was photographed periodically, and the colored images were subsequently converted to grayscale images and then digitally analyzed to determine the standardized grayscale values (G0) by comparing with that of standard color strip. The G0 of a sample at each time of photographing during bleaching was divided by the difference of G0 between the acclimating and the same but completely bleached fragment to derive the relative grayscale (RG%) at a particular stage of bleaching; this is done for each coral fragment of a colony. The smaller the RG% of a coral fragment the closer it is approaching completely bleached condition. The level of decrease in RG% within a time series of images in each heating regime was used to establish a bleaching time index (BTI). The lower the BTI, the sooner to reach a defined bleaching level (e.g., 30%), this indicates the coral is more sensitive to thermal bleaching. In the experiment, we compared the bleaching susceptibility of the five species. Based on the proposed BTI, the five species were ranked in terms of bleaching susceptibility, and the rankings were identical between the two temperature regimes; three species in Pocilloporidae had lower BTI, where…
bibliographic citation: Wang et al. (2022) Comparison of the bleaching susceptibility of coral species by using minimal samples of live corals. PeerJ 10:e12840 https://doi.org/10.7717/peerj.12840
date submitted: 2021-09-01
date accepted: 2022-01-06
issued: 2022-01-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Jih-Terng
author list: Agent
  family name: Chu
  given name: Chi-Wei
author list: Agent
  family name: Soong
  given name: Keryea
doi: 10.7717/peerj.12840
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-26
copyright: © 2022 Wang et al.
attribution name: Wang et al.

Potential impacts from simulated vessel noise and sonar on commercially important invertebrates
type: item
type: AcademicArticle
description: Human usage of coastal water bodies continues to increase and many invertebrates face a broad suite of anthropogenic stressors (e.g., warming, pollution, acidification, fishing pressure). Underwater sound is a stressor that continues to increase in coastal areas, but the potential impact on invertebrates is not well understood. In addition to masking natural sound cues which may be important for behavioral interactions, there is a small but increasing body of scientific literature indicating sublethal physiological stress may occur in invertebrates exposed to high levels of underwater sound, particularly low frequency sounds such as vessel traffic, construction noise, and some types of sonar. Juvenile and sub-adult blue crabs (Callinectes sapidus) and American lobsters (Homarus americanus) were exposed to simulated low-frequency vessel noise (a signal was low-pass filtered below 1 kHz to ensure low-frequency content only) and mid-frequency sonar (a 1-s 1.67 kHz continuous wave pulse followed by a 2.5 to 4.0 kHz 1-s linear frequency modulated chirp) and behavioral response (the animal’s activity level) was quantified during and after exposure using EthoVision XT™ from overhead video recordings. Source noise was quantified by particle acceleration and pressure. Physiological response to the insults (stress and recovery) were also quantified by measuring changes in hemolymph heat shock protein (HSP27) and glucose over 7 days post-exposure. In general, physiological indicators returned to baseline levels within approximately 48 h, and no observable difference in mortality between treatment and control animals was detected. However, there was a consistent amplified hemolymph glucose signal present 7 days after exposure for those animals exposed to mid-frequency sound and there were changes to C. sapidus competitive behavior within 24 h of exposure to sound. These results stress the importance of considering the impacts of underwater sound among the suite of stressors fac…
format: application/pdf
format: text/html
creator: David M. Hudson
creator: Jason S. Krumholz
creator: Darby L. Pochtar
creator: Natasha C. Dickenson
creator: Georges Dossot
creator: Gillian Phillips
creator: Edward P. Baker
creator: Tara E. Moll
subject: Animal Behavior
subject: Ecology
subject: Marine Biology
subject: Environmental Impacts
subject: Biological Oceanography
description: doi:10.7717/peerj.12841
publisher: PeerJ Inc.
rights: © 2022 Hudson et al.
abstract: Human usage of coastal water bodies continues to increase and many invertebrates face a broad suite of anthropogenic stressors (e.g., warming, pollution, acidification, fishing pressure). Underwater sound is a stressor that continues to increase in coastal areas, but the potential impact on invertebrates is not well understood. In addition to masking natural sound cues which may be important for behavioral interactions, there is a small but increasing body of scientific literature indicating sublethal physiological stress may occur in invertebrates exposed to high levels of underwater sound, particularly low frequency sounds such as vessel traffic, construction noise, and some types of sonar. Juvenile and sub-adult blue crabs (Callinectes sapidus) and American lobsters (Homarus americanus) were exposed to simulated low-frequency vessel noise (a signal was low-pass filtered below 1 kHz to ensure low-frequency content only) and mid-frequency sonar (a 1-s 1.67 kHz continuous wave pulse followed by a 2.5 to 4.0 kHz 1-s linear frequency modulated chirp) and behavioral response (the animal’s activity level) was quantified during and after exposure using EthoVision XT™ from overhead video recordings. Source noise was quantified by particle acceleration and pressure. Physiological response to the insults (stress and recovery) were also quantified by measuring changes in hemolymph heat shock protein (HSP27) and glucose over 7 days post-exposure. In general, physiological indicators returned to baseline levels within approximately 48 h, and no observable difference in mortality between treatment and control animals was detected. However, there was a consistent amplified hemolymph glucose signal present 7 days after exposure for those animals exposed to mid-frequency sound and there were changes to C. sapidus competitive behavior within 24 h of exposure to sound. These results stress the importance of considering the impacts of underwater sound among the suite of stressors fac…
bibliographic citation: Hudson et al. (2022) Potential impacts from simulated vessel noise and sonar on commercially important invertebrates. PeerJ 10:e12841 https://doi.org/10.7717/peerj.12841
date submitted: 2021-02-04
date accepted: 2022-01-06
issued: 2022-01-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hudson
  given name: David M.
author list: Agent
  family name: Krumholz
  given name: Jason S.
author list: Agent
  family name: Pochtar
  given name: Darby L.
author list: Agent
  family name: Dickenson
  given name: Natasha C.
author list: Agent
  family name: Dossot
  given name: Georges
author list: Agent
  family name: Phillips
  given name: Gillian
author list: Agent
  family name: Baker
  given name: Edward P.
author list: Agent
  family name: Moll
  given name: Tara E.
doi: 10.7717/peerj.12841
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-26
copyright: © 2022 Hudson et al.
attribution name: Hudson et al.

Isolation, identification and characterization of nitrogen fixing endophytic bacteria and their effects on cassava production
type: item
type: AcademicArticle
description: Background Cassava (Manibot esculenta Crantz) is one of the most important among tuber crops. The amount of nitrogen fertilizer used for cassava production is relatively high (400 kg ha−1), but there are few studies on biological nitrogen fixation in this crop. Therefore, it is particularly important to study whether cassava and microorganisms have the associated nitrogen-fixing and other promoting effects of endophytic bacteria. Methods We screened 10 endophytic bacteria using the nitrogen-free culture method from the roots of seven cassava cultivars, and the nitrogenase activity of the A02 strain was the highest 95.81 nmol mL−1 h−1. The A02 strain was confirmed as Microbacteriaceae, Curtobacterium using 16S rRNA sequence alignment. The biological and morphological characteristics of strain A02 were further analyzed. Results The experimental results showed that the biomass of roots, stems, and leaves of cassava inoculated with A02 increased by 17.6%, 12.6%, and 10.3%, respectively, compared to that of the control (without A02 inoculation). These results were not only related to the secretion of auxin (IAA) and solubilization of phosphate but also in the promotion of biological nitrogen fixation of cassava leaves by strain A02. Moreover, the highest 95.81 nmol mL−1h−1 of nitrogenase activity was reported in strain A02, and thus more nitrogen fixation was observed in strain A02. In conclusion, A02 is a newly discovered endophytic nitrogen-fixing bacteria in cassava that can be further used in the research of biological bacterial fertilizers.
format: application/pdf
format: text/html
creator: Xiao Zhang
creator: Juanjuan Tong
creator: Mengmeng Dong
creator: Kashif Akhtar
creator: Bing He
subject: Agricultural Science
subject: Natural Resource Management
description: doi:10.7717/peerj.12677
publisher: PeerJ Inc.
rights: © 2022 Zhang et al.
abstract: Background Cassava (Manibot esculenta Crantz) is one of the most important among tuber crops. The amount of nitrogen fertilizer used for cassava production is relatively high (400 kg ha−1), but there are few studies on biological nitrogen fixation in this crop. Therefore, it is particularly important to study whether cassava and microorganisms have the associated nitrogen-fixing and other promoting effects of endophytic bacteria. Methods We screened 10 endophytic bacteria using the nitrogen-free culture method from the roots of seven cassava cultivars, and the nitrogenase activity of the A02 strain was the highest 95.81 nmol mL−1 h−1. The A02 strain was confirmed as Microbacteriaceae, Curtobacterium using 16S rRNA sequence alignment. The biological and morphological characteristics of strain A02 were further analyzed. Results The experimental results showed that the biomass of roots, stems, and leaves of cassava inoculated with A02 increased by 17.6%, 12.6%, and 10.3%, respectively, compared to that of the control (without A02 inoculation). These results were not only related to the secretion of auxin (IAA) and solubilization of phosphate but also in the promotion of biological nitrogen fixation of cassava leaves by strain A02. Moreover, the highest 95.81 nmol mL−1h−1 of nitrogenase activity was reported in strain A02, and thus more nitrogen fixation was observed in strain A02. In conclusion, A02 is a newly discovered endophytic nitrogen-fixing bacteria in cassava that can be further used in the research of biological bacterial fertilizers.
bibliographic citation: Zhang et al. (2022) Isolation, identification and characterization of nitrogen fixing endophytic bacteria and their effects on cassava production. PeerJ 10:e12677 https://doi.org/10.7717/peerj.12677
date submitted: 2021-09-06
date accepted: 2021-12-02
issued: 2022-01-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Xiao
author list: Agent
  family name: Tong
  given name: Juanjuan
author list: Agent
  family name: Dong
  given name: Mengmeng
author list: Agent
  family name: Akhtar
  given name: Kashif
author list: Agent
  family name: He
  given name: Bing
doi: 10.7717/peerj.12677
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-25
copyright: © 2022 Zhang et al.
attribution name: Zhang et al.

Diversity and structure of the microbial community in rhizosphere soil of Fritillaria ussuriensis at different health levels
type: item
type: AcademicArticle
description: Fritillaria wilt is a kind of soil-borne disease that causes a large reduction in the yield of Fritillaria ussuriensis. The diversity and structure of the soil microbial community are important factors affecting the health of Fritillaria ussuriensis. The analysis of the microbial community in the diseased and healthy soils provided a theoretical basis for revealing the pathological mechanism and prevention of Fritillaria wilt disease. In the present study, we sequenced the soil microorganisms from healthy (H), pathology (P) and blank (B) soil samples by Illumina MiSeq. Determined the soil physicochemical properties respectively, analyzed the soil microbial diversity and structure, and constructed single factor co-correlation networks among microbial genera. The results showed that Ascomycota (48.36%), Mortierellomycota (23.06%), Basidiomycota (19.00%), Proteobacteria (31.74%), and Acidobacteria (20.95%) were dominant in the soil. The diversity of healthy soil was significantly greater than that of diseased soil samples (P and B) (P < 0.05). The populations of Fusarium and Humicola significantly increased in the diseased soil sample (P and B) (P < 0.05). RB41 (4.74%) and Arthrobacter (3.30%) were the most abundant genera in the healthy soil. Total nitrogen (TN), available nitrogen (AN), total potassium (TK), available potassium (AK), and inorganic salt (salt) were significantly correlated with soil microbial communities (P < 0.05). The relationship between fungi and the plant was mostly positive, whereas bacteria showed the opposite trend. In conclusion, the diversity and structure of the soil microbial community were closely related to the health level of Fritillaria ussuriensis. Fusarium and Humicola affect the severity of Fritillaria wilt disease, while RB41 and Arthrobacter are the important indicators for maintaining the health of Fritillaria ussuriensis. Moreover, environmental factors greatly affect the abundance and formation of soil microbial community. The …
format: application/pdf
format: text/html
creator: Ning Jiao
creator: Xiaoshuang Song
creator: Ruiqing Song
creator: Dachuan Yin
creator: Xun Deng
subject: Microbiology
subject: Molecular Biology
subject: Plant Science
subject: Soil Science
subject: Biogeochemistry
description: doi:10.7717/peerj.12778
publisher: PeerJ Inc.
rights: © 2022 Jiao et al.
abstract: Fritillaria wilt is a kind of soil-borne disease that causes a large reduction in the yield of Fritillaria ussuriensis. The diversity and structure of the soil microbial community are important factors affecting the health of Fritillaria ussuriensis. The analysis of the microbial community in the diseased and healthy soils provided a theoretical basis for revealing the pathological mechanism and prevention of Fritillaria wilt disease. In the present study, we sequenced the soil microorganisms from healthy (H), pathology (P) and blank (B) soil samples by Illumina MiSeq. Determined the soil physicochemical properties respectively, analyzed the soil microbial diversity and structure, and constructed single factor co-correlation networks among microbial genera. The results showed that Ascomycota (48.36%), Mortierellomycota (23.06%), Basidiomycota (19.00%), Proteobacteria (31.74%), and Acidobacteria (20.95%) were dominant in the soil. The diversity of healthy soil was significantly greater than that of diseased soil samples (P and B) (P < 0.05). The populations of Fusarium and Humicola significantly increased in the diseased soil sample (P and B) (P < 0.05). RB41 (4.74%) and Arthrobacter (3.30%) were the most abundant genera in the healthy soil. Total nitrogen (TN), available nitrogen (AN), total potassium (TK), available potassium (AK), and inorganic salt (salt) were significantly correlated with soil microbial communities (P < 0.05). The relationship between fungi and the plant was mostly positive, whereas bacteria showed the opposite trend. In conclusion, the diversity and structure of the soil microbial community were closely related to the health level of Fritillaria ussuriensis. Fusarium and Humicola affect the severity of Fritillaria wilt disease, while RB41 and Arthrobacter are the important indicators for maintaining the health of Fritillaria ussuriensis. Moreover, environmental factors greatly affect the abundance and formation of soil microbial community. The …
bibliographic citation: Jiao et al. (2022) Diversity and structure of the microbial community in rhizosphere soil of Fritillaria ussuriensis at different health levels. PeerJ 10:e12778 https://doi.org/10.7717/peerj.12778
date submitted: 2021-08-17
date accepted: 2021-12-21
issued: 2022-01-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiao
  given name: Ning
author list: Agent
  family name: Song
  given name: Xiaoshuang
author list: Agent
  family name: Song
  given name: Ruiqing
author list: Agent
  family name: Yin
  given name: Dachuan
author list: Agent
  family name: Deng
  given name: Xun
doi: 10.7717/peerj.12778
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-01-25
copyright: ©2022 Jiao et al.
attribution name: Jiao et al.

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359